3EID | pdb_00003eid

CDK2/CyclinA complexed with a pyrazolopyridazine inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FVV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	277	1.5 M sodium acetate, 100 mM sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.1	70.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 184.506	α = 90
b = 184.506	β = 90
c = 213.302	γ = 120

Symmetry
Space Group	P 62 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2001-08-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	3.15	19.99	89.2	0.09	21	4.9		31913	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.15	3.23	91		0.51	3.8		2378

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1FVV	3.15	19.99	31913	31913	1654	89.2	0.20702	0.20702	0.20422	0.26071	0.2743	RANDOM	84.483

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
2.56	1.28		2.56		-3.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.307
r_dihedral_angle_3_deg	15.225
r_dihedral_angle_4_deg	14.623
r_dihedral_angle_1_deg	4.921
r_angle_refined_deg	1.049
r_scangle_it	0.987
r_scbond_it	0.574
r_mcangle_it	0.495
r_nbtor_refined	0.301
r_mcbond_it	0.268
r_nbd_refined	0.187
r_xyhbond_nbd_refined	0.164
r_symmetry_hbond_refined	0.163
r_symmetry_vdw_refined	0.158
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8664
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing